Purpose: Four-dimensional computed tomography (4D-CT) has been widely used in radiation therapy to assess patient-specific breathing motion for determining individual safety margins. However, it has two major drawbacks: low soft-tissue contrast and an excessive imaging dose to the patient. This research aimed to develop a clinically feasible four-dimensional magnetic resonance imaging (4D-MRI) technique to overcome these limitations. Methods: The proposed 4D-MRI technique was achieved by continuously acquiring axial images throughout the breathing cycle using fast 2D cine-MR imaging, and then retrospectively sorting the images by respiratory phase. The key component of the technique was the use of body area (BA) of the axial MR images as an internal respiratory surrogate to extract the breathing signal. The validation of the BA surrogate was performed using 4D-CT images of 12 cancer patients by comparing the respiratory phases determined using the BA method to those determined clinically using the Real-time position management (RPM) system. The feasibility of the 4D-MRI technique was tested on a dynamic motion phantom, the 4D extended Cardiac Torso (XCAT) digital phantom, and two healthy human subjects. Results: Respiratory phases determined from the BA matched closely to those determined from the RPM: mean (6SD) difference in phase: À3.9% (66.4%); mean (6SD) absolute difference in phase: 10.40% (63.3%); mean (6SD) correlation coefficient: 0.93 (60.04). In the motion phantom study, 4D-MRI clearly showed the sinusoidal motion of the phantom; image artifacts observed were minimal to none. Motion trajectories measured from 4D-MRI and 2D cine-MRI (used as a reference) matched excellently: the mean (6SD) absolute difference in motion amplitude: À0.3 (60.5) mm. In the 4D-XCAT phantom study, the simulated "4D-MRI" images showed good consistency with the original 4D-XCAT phantom images. The motion trajectory of the hypothesized "tumor" matched excellently between the two, with a mean (6SD) absolute difference in motion amplitude of 0.5 (60.4) mm. 4D-MRI was able to reveal the respiratory motion of internal organs in both human subjects; superior-inferior (SI) maximum motion of the left kidney of Subject #1 and the diaphragm of Subject #2 measured from 4D-MRI was 0.88 and 1.32 cm, respectively. Conclusions: Preliminary results of our study demonstrated the feasibility of a novel retrospective 4D-MRI technique that uses body area as a respiratory surrogate.

We present a new de novo transcriptome assembler, Bridger, which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers. When tested on dog, human, and mouse RNA-seq data, Bridger assembled more full-length reference transcripts while reporting considerably fewer candidate transcripts, hence greatly reducing false positive transcripts in comparison with the state-of-the-art assemblers. It runs substantially faster and requires much less memory space than most assemblers. More interestingly, Bridger reaches a comparable level of sensitivity and accuracy with Cufflinks. Bridger is available at https://sourceforge.net/projects/rnaseqassembly/files/?source=navbar.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0596-2) contains supplementary material, which is available to authorized users.

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The commissioning data indicated good consistency among the three TB-LINAC units. The commissioning data provided us valuable insights and reliable evaluations on the characteristics of the new treatment system. The systematically measured data might be useful for future reference.

We studied frog biodiversity along an elevational gradient in the Hengduan Mountains, China. Endemic and non‐endemic elevational diversity patterns were examined individually. Competing hypotheses were also tested for these patterns. Species richness of total frogs, endemics and non‐endemics peaked at mid‐elevations. The peak in endemic species richness was at higher elevations than the maxima of total species richness. Endemic species richness followed the mid‐domain model predictions, and showed a nonlinear relationship with temperature. Water and energy were the most important variables in explaining elevational patterns of non‐endemic species richness. A suite of interacting climatic and geometric factors best explained total species richness patterns along the elevational gradient. We suggest that the mid‐domain effect was an important factor to explain elevational richness patterns, especially in regions with high endemism.